Individuals from high-risk breast cancer families comprise about 10% of incident cases. Among these individuals, germline mutations in the BRCA1 and BRCA2 genes can be detected in 20-40% of cases (TONIN et al., Nature Medicine, 2:1179-1183 (1997)). Other moderate to high penetrance genes contribute to heritable breast cancer predisposition (MANNUCCI et al., Chemosphere, (2012)). These genes tend to share common pathways with BRCA1 and 2 and play a role in the repair of double-stranded breaks in DNA. Homozygous mutations in some of these genes cause Fanconi anemia (FA), ataxia telangiectasia and Nijmegen breakage syndrome. The 14 FA genes work together in concert with BRCA1 in a common DNA repair pathway and, if mutated, convey risk for breast cancer. In response to DNA damage (FIG. 1), ATM (ataxia telangiectasia mutated) and ATR (ataxia telangiectasia and Rad3-related) kinases activate the FA core complex comprising FANCA, B, C, E, F, G, L, and M, which then monoubiquinates FANCD2 and FANCI. This complex then interacts with other downstream proteins, FANCD1 (BRCA2), FANCN (PALB2), and FANCJ (BRIP1) to initiate DNA repair through homologous recombination. BRCA1 has also been identified as an upstream regulator of the PALB2/BRCA2 complex, promoting its localization to DNA damage sites (CASADEI et al., Cancer Res, 71:2222-2229 (2011)). BRCA1 exists mostly as a heterodimer with BARD1 forming a ubiquitin ligase that is instrumental in BRCA1 response to DNA damage (STARITA et al., Cancer Biol Ther 5:137-141 (2006)). PALB2, BRIP1, and BARD1 gene mutations have been associated with increased risk of breast cancer (SEAL et al., Nat Genet 38:1239-1241 (2006); STACEY et al., PLoS Med 3:e217 (2006)).
Nijmegen breakage syndrome is an autosomal recessive chromosome instability syndrome of microcephaly, growth retardation, intellectual disability, immunodeficiency, and increased risk of malignancy, caused by mutations in the NBN gene (BOGDANOVA et al., Int J Cancer, 122:802-806 (2008)). NBN forms a complex with MRE11A and RAD50 to form the Mre11 complex necessary for DNA double stranded break repair (HEIKKINEN et al., Carcinogenesis, 27:1593-1599 (2006); DESJARDINS et al., BMC Cancer, 9:181 (2009)). This complex co-localizes with BRCA1 as well as with FANCD2 in response to DNA damage (WANG et al., Genes Dev, 14:927-939 (2000)). Heterozygous mutations in NBN, MRE11A, or RAD50 have been found to be associated with increased risk of breast cancer (BOGDANOVA et al., Int J Cancer, 122:802-806 (2008); HEIKKINEN et al., Carcinogenesis, 27:1593-1599 (2006); HSU et al., Cancer Epidemiol Biomarkers Prev, 16:2024-2032 (2007)).
Informatics approaches have been taken for curating newly identified genetic variants to determine whether they are pathogenic. These informatics approaches combine prior probabilities of causality derived from an evolutionary sequence conservation model (Align-GVGD) with the likelihood of how the variant segregates with cancer in sequenced families, whether the variant is seen in combination with a known pathogenic mutation (which should be lethal for BRCA1 or cause FA for BRCA2, if the variant is pathogenic), the age of onset and cancer type associated with the variant, and the histology of the associated breast tumors. The accuracy of the Align-GVGD method may be high; however, it requires sequencing for calling variants and may overweigh high-penetrance variants, since moderate penetrance variants would simply not show the co-transmission with the cancer phenotype.